Comments (4)
jma1991
commented on July 19, 2024
1
Hello @paolo-kunderfranco
After some investigation, it seems the error is not specific to the pipeline or its operation but the underlying stageR package. I have opened an issue with the original developer here to see if we can work together to address the issue.
Thanks,
James
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jma1991
commented on July 19, 2024
Hello @paolo-kunderfranco
Please could you send the input files which are passed to the run_stage.R script where the error occurs. With the input files, we can run the script by hand and de-bug why the error has occurred.
Thank you,
James
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paolo-kunderfranco
commented on July 19, 2024
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paolo-kunderfranco
commented on July 19, 2024
no news?
Up to now I add --dexseq_dtu false to terminate the workflow
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Related Issues (20)
- link to example contrastsheet.csv is not working HOT 1
- Empty output for BAM+rMats HOT 2
- make contrasts file names consistent with those of the differentialabundance pipeline HOT 1
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- STAGER error: subscript out of bounds HOT 6
- The pipeline should be able to infer strandedness from FASTQ (i.e. allow "auto" for strandedness in the CSV) HOT 2
- Error with rmats.py when running with multiple contrasts: <filename>.bam not found in .rmats files HOT 10
- MISO_SASHIMI error: Could not find MISO output files HOT 4
- test profile: miso_index failure HOT 19
- example contrastsheet.csv missing HOT 1
- Add some more tags to make the pipeline easier to find HOT 1
- DRIMSEQ_FILTER error HOT 5
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